Bittner L. auteur aut IRD Halary S. auteur aut IRD Payri Claude auteur aut IRD Cruaud C. auteur aut IRD Reviers de B. auteur aut IRD Lopez P. auteur aut IRD Bapteste E. auteur aut IRD text journalArticle eng text/pdf born digital access Background: Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution. Presentation of the hypothesis: We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments. Testing the hypothesis: We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies. Implications of the hypothesis: Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta) transcriptomic and (meta) proteomic data. Reviewers: This article was reviewed by Pr. William Martin, Dr. David Williams (nominated by Pr. J Peter Gogarten) & Dr. James McInerney (nominated by Pr. John Logsdon). specialized 020 021 5 47 2010 1745-6150 https://www.documentation.ird.fr/hor/fdi:010049037 10.1186/1745-6150-5-47 1745-6150 [F B010049037] https://www.documentation.ird.fr/hor/fdi:010049037 https://www.documentation.ird.fr/intranet/publi/2010/09/010049037.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2010-10-01 2017-08-23 fdi:010049037 fre